Inferring species trees given coalescence and reticulation Mike Pirie, University of Stellenbosch Abstract For evolutionary biologists seeking to infer relatedness of organisms – the ‘species tree’ – the current paradigm can be summed up in one word: coalescence. It is clear that gene trees differences are biologically meaningful (give or take analytical error) and should be exploited to accurately recover the sequence and timing of speciation events. However, whilst coalescent stochasticity is not the only process underlying species tree/gene tree discordance, it currently serves as the null hypothesis: assumed, given the (common) circumstances under which it cannot be rejected. This approach serves to bias against inferring reticulate processes (such as hybridisation), even though they may be common and of direct importance both for the evolutionary process itself and the performance of methods used to infer it. I use examples from both plant and virus datasets to demonstrate an easily implemented supermatrix approach that is not dependent on the assumption of an underlying bifurcating species tree. This approach may be used to infer the sequence and timing of gene and genome divergences given conflict between individual gene trees, even when the processes underlying that conflict cannot be distinguished. It can in principle be applied to any group of organisms and can be extended to explicitly model both reticulation and coalescence without prior knowledge of the species tree topology. 25 Feb 2013, 15.00-16.00, Seminar room 232b, Botaniska Institutionen, Lilla Frescativägen 5, SE-10691 All welcome! Aelys Humphreys & Catarina Rydin /JN |
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